Exam 3 - Lecture 6

Question 1

Know how we name enzymes

Answer 1

(e.g. ____ dependent ____ polymerase)

Question 2

You need to understand the basic concepts of cellular transcription and translation.

Answer 2

transcription: information in DNA is copied into a complementary RNA

translation: ribosome reads mRNA codon sequence and makes a polypeptide – same for all viruses

Question 3

Double-stranded DNA viruses
- Where do they usually replicate in the cell and why?
- What enzyme is used for transcription and its genome replication?

Answer 3

• replicate in the nucleus
• cellular DNA-dependent RNA polymerase is used for transcription

Question 4

Why do DNA viruses mutate at a relatively slow rate?

Answer 4

their proofreading ability intended to prevent mistakes

Question 5

Single-stranded DNA viruses
- Where in the cell do they do transcription and genome replication?
- What extra step must occur before transcription takes place?
- What enzyme does this extra step?

Answer 5

• transcription and replication occur in the nucleus
• ssDNA viruses must use cellular
  DNA-dependent DNA polymerase
  enzymes to make the 2nd strand
  first

Question 6

Single-stranded DNA viruses
- What enzymes do transcription and genome replication?
- What is different about its genome replication when compared to dsDNA viruses?

Answer 6

• cellular DNA-dependent RNA polymerase is used for transcription and genome replication
• the dsDNA intermediate used for genome replication

Question 7

RNA viruses
- Where do they usually replicate?
- What type of enzyme do they need to replicate their genome and where does that enzyme come from?
- What is commonly wrong with this enzyme?

Answer 7

• replicate in the cytosol
• they have to make their own RNA-dependent RNA polymerase, which is much more prone to error than cellular enzymes (bc they lack proofreading ability)

Question 8

Double-stranded RNA viruses
- How is its genome transcribed?
- Besides being double-stranded, what is a common feature of their genomes?

Answer 8

these viruses often have segmented genomes, so transcription will have to repeat with each section

Question 9

Double-stranded RNA viruses
- How do cells respond to dsRNA and what are some proteins they use for this response?
- How do dsRNA viruses get around the cellular “immune” response?

Answer 9

• most cells have developed mechanisms to detect and destroy dsRNA as a host defense (using proteins such as PKR and MDA5)
• dsRNA viruses get around this response by transcribing the RNA genome while still in the capsid before uncaring, and by having RdRp within the virion itself

Question 10

Double-stranded RNA viruses
- What exactly gets packaged into new capsids (in terms of the genome) and how is that transformed while inside the capsid?

Answer 10

along with the transcribed RNA genome, positive sense RNA strands from this transcription will also be packaged into the new capsid

Question 11

Positive sense ssRNA viruses
- What do their genomes look like and what happens to them upon entering into the host cell?

Answer 11

Positive sense RNA virus genomes resemble mRNA

Upon entry, the genome is translated directly by ribosomes

Question 12

Positive sense ssRNA viruses
- What is usually one of the first proteins made?

Answer 12

RdRp

Question 13

Positive sense ssRNA viruses
- How are more genomes made?

Answer 13

RdRp uses the dsRNA to make more positive sense (mRNA) strands, and those mRNAs are used to make more viral protein and serve as new genomes

Question 14

Positive sense ssRNA viruses
- Why do these viruses sometimes make shorter RNA pieces (sub-genomic)? What does it use those for?

Answer 14

The shorter RNA pieces created by positive sense ssRNA viruses are used to make new kinds of viral proteins

Question 15

Negative sense ssRNA viruses
- What does the genome look like and why does it have to be copied by the RdRp before anything else happens? Where does this copying event take place?

Answer 15

Negative sense ssRNA viruses do not resemble mRNA, and must be transcribed into positive sense strands

This process takes place in a protected membrane invagination

Question 16

Negative sense ssRNA viruses
- Know what the mRNAs look like and how it produces more genome

Answer 16

the viral mRNAs look like short, positive sense strands that are capped

The negative sense strand is used by the RdRp to make a full-length positive sense RNA that will then be copied to make copies of negative sense genomes

Question 17

Retroviruses (RNA)
- What are the functions of RT and integrase?

Answer 17

RT copies the ssRNA genome into a complementary ssDNA negative strand

Integrase is an enzyme that inserts the dsDNA viral genome into a host DNA genome

Question 18

Retroviruses (RNA)
- You need to have a good understanding of the reverse transcription process

Answer 18

1) Cellular tRNA binds to a primer binding site at the end of viral RNA
2) as new piece of DNA are being made, they come off and move to the opposite end of the RNA genome (1st strand switch)
3) RT finishes the first strand of DNA
4) RT destroys most of the RNA genome except for a small piece called PPT, which is then used as a primer to make the second strand of DNA
5) that piece comes off and moves to the opposite end of the strand (second strand switch)
6) RT makes the rest of the 2nd strand of DNA

Question 19

Retroviruses (RNA)
- Once the viral genome is in the host genome, how does the virus make more genome and make protein?

Answer 19

Transcription makes new viral proteins

Viral and host transcription factors bind to viral promoters, and host RNA polymerase makes positive sense viral mRNA
- some of this new positive sense mRNA will be used for new genomes

Question 20

Retroviruses (DNA)
- What do their genomes look like?

Answer 20

Retrovirus genomes are partially dsDNA

Question 21

Retroviruses (DNA)
- How do these viruses do transcription?

Answer 21

Host RNA polymerases transcribe all of the viral genes, and a full-length mRNA copy of the entire genome to package into new capsids

Question 22

Retroviruses (DNA)
- What does the RT enzyme do in these viruses?

Answer 22

RT will bind to the mRNA and make a DNA copy from it in order to make 1 full strand and a 2nd partial strand of DNA